Bio::SeqFeature::Annotated - PLEASE PUT SOMETHING HERE
# none yet, complain to authors
None yet, complain to authors.
This class implementes the following interfaces.
Note that this includes implementing Bio::RangeI.
Features held by a feature are essentially sub-features.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
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Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
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Allen Day <allenday at ucla.edu>
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Usage: $obj->from_feature($myfeature); Desc : initialize this object with the contents of another feature object. Useful for converting objects like L<Bio::SeqFeature::Generic> to this class Ret : nothing meaningful Args : a single object of some other feature type, Side Effects: throws error on failure Example:
Usage : $obj->seq_id($newval) Function: holds a string corresponding to the unique seq_id of the sequence underlying the feature (e.g. database accession or primary key). Returns : a Bio::Annotation::SimpleValue object representing the seq_id. Args : on set, some string or a Bio::Annotation::SimpleValue object.
Usage : $obj->name($newval) Function: human-readable name for the feature. Returns : value of name (a scalar) Args : on set, new value (a scalar or undef, optional)
Usage : $obj->type($newval) Function: a SOFA type for the feature. Returns : Bio::Annotation::OntologyTerm object representing the type. Args : on set, a SOFA name, identifier, or Bio::Annotation::OntologyTerm object.
Usage : $obj->source($newval) Function: holds a string corresponding to the source of the feature. Returns : a Bio::Annotation::SimpleValue object representing the source. Args : on set, some scalar or a Bio::Annotation::SimpleValue object.
Usage : $score = $feat->score() $feat->score($score) Function: holds a value corresponding to the score of the feature. Returns : a Bio::Annotation::SimpleValue object representing the score. Args : on set, a scalar or a Bio::Annotation::SimpleValue object.
Usage : $phase = $feat->phase() $feat->phase($phase) Function: get/set on phase information Returns : a Bio::Annotation::SimpleValue object holdig one of 0,1,2,'.' as its value. Args : on set, one of 0,1,2,'.' or a Bio::Annotation::SimpleValue object holding one of 0,1,2,'.' as its value.
Usage : $frame = $feat->frame() $feat->frame($phase) Function: get/set on phase information Returns : a Bio::Annotation::SimpleValue object holdig one of 0,1,2,'.' as its value. Args : on set, one of 0,1,2,'.' or a Bio::Annotation::SimpleValue object holding one of 0,1,2,'.' as its value.
Usage : Function: $obj->add_Annotation() is a shortcut to $obj->annotation->add_Annotation Returns : Args :
Usage : Function: $obj->remove_Annotations() is a shortcut to $obj->annotation->remove_Annotations Returns : Args :
Deprecated, use L<Bio::SeqFeatureI/name()>. Will raise a warning.
Deprecated, use L<Bio::SeqFeatureI/type()>. Will raise a warning.
Deprecated, use L<Bio::SeqFeatureI/source()>. Will raise a warning.
Usage : $sf->attach_seq($seq) Function: Attaches a Bio::Seq object to this feature. This Bio::Seq object is for the *entire* sequence: ie from 1 to 10000 Returns : TRUE on success Args : a Bio::PrimarySeqI compliant object
Usage : $tseq = $sf->seq() Function: returns a truncated version of seq() with bounds matching this feature Returns : sub seq (a Bio::PrimarySeqI compliant object) on attached sequence bounded by start & end, or undef if there is no sequence attached Args : none
Usage : $whole_seq = $sf->entire_seq() Function: gives the entire sequence that this seqfeature is attached to Returns : a Bio::PrimarySeqI compliant object, or undef if there is no sequence attached Args : none
See Bio::AnnotatableI::has_tag().
See Bio::AnnotatableI::add_tag_value().
See Bio::AnnotationCollectionI::get_tag_values().
See Bio::AnnotationCollectionI::get_all_annotation_keys().
See Bio::AnnotationCollectionI::remove_tag().
as inherited via Bio::SeqFeatureI
Usage : $feature->length() Function: Get the feature length computed as $feat->end - $feat->start + 1 Returns : integer Args : none
Usage : $obj->start($newval) Function: Get/set on the start coordinate of the feature Returns : integer Args : on set, new value (a scalar or undef, optional)
Usage : $obj->end($newval) Function: Get/set on the end coordinate of the feature Returns : integer Args : on set, new value (a scalar or undef, optional)
Usage : $strand = $feat->strand($newval) Function: get/set on strand information, being 1,-1 or 0 Returns : -1,1 or 0 Args : ???
This includes methods for retrieving, adding, and removing features. Since this is already a feature, features held by this feature holder are essentially sub-features.
Usage : @feats = $feat->get_SeqFeatures(); Function: Returns an array of Bio::SeqFeatureI objects Returns : An array Args : none
Usage : $feat->add_SeqFeature($subfeat); $feat->add_SeqFeature($subfeat,'EXPAND') Function: adds a SeqFeature into the subSeqFeature array. with no 'EXPAND' qualifer, subfeat will be tested as to whether it lies inside the parent, and throw an exception if not. If EXPAND is used, the parent''s start/end/strand will be adjusted so that it grows to accommodate the new subFeature Example : Returns : nothing Args : a Bio::SeqFeatureI object
Usage : $obj->remove_SeqFeatures Function: Removes all sub SeqFeatures. If you want to remove only a subset, remove that subset from the returned array, and add back the rest. Returns : The array of Bio::SeqFeatureI implementing sub-features that was deleted from this feature. Args : none
Usage : $obj->annotation($annot_obj) Function: Get/set the annotation collection object for annotating this feature. Returns : A Bio::AnnotationCollectionI object Args : newvalue (optional)
Usage : my $location = $seqfeature->location() Function: returns a location object suitable for identifying location of feature on sequence or parent feature Returns : Bio::LocationI object Args : [optional] Bio::LocationI object to set the value to.
Usage : $seqfeature->add_target(Bio::LocatableSeq->new(...)); Function: adds a target location on another reference sequence for this feature Returns : true on success Args : a Bio::LocatableSeq object
Usage : @targets = $seqfeature->each_target(); Function: Returns a list of Bio::LocatableSeqs which are the locations of this object. To obtain the "primary" location, see L</location()>. Returns : a list of 0..N Bio::LocatableSeq objects Args : none
Title : _expand_region Usage : $self->_expand_region($feature); Function: Expand the total region covered by this feature to accomodate for the given feature. May be called whenever any kind of subfeature is added to this feature. add_SeqFeature() already does this. Returns : Args : A Bio::SeqFeatureI implementing object.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.